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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ), 'gf_id' => 'HOM05D001382', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001382' ), 'data_identifier' => 'HOM05D001382', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001382', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p33890' => 'bna', 'Aa31LG1G2950' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1384' => 'aag', 'Actinidia05487' => 'ach', 'Actinidia07400' => 'ach', 'Actinidia11855' => 'ach', 'Actinidia13329' => 'ach', 'Actinidia32662' => 'ach', 'Ah.16g105670' => 'amhyb', 'AL1G23010' => 'aly', 'AL2G25800' => 'aly', 'Aqoxy1G02092' => 'aox', 'Aqoxy1G04215' => 'aox', 'Aqoxy3G00471' => 'aox', 'Aqoxy4G01865' => 'aox', 'Aqoxy7G01511' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07VZ9L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0U8GU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1M918L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2N5SYE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4AF6N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56DA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.71VUPL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8TCK1P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9E4RBZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BI5I0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRPI7U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIXS0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJJR8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L3087Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LHN4XV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MGTB4W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MLQ69B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UGG0Q6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YSX6Q2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQR06K' => 'arhy', 'AT1G11840' => 'ath', 'AT1G67280' => 'ath', 'ATR0315G002' => 'atr', 'ATR0794G002' => 'atr', 'Atru.chr10.2241' => 'acertr', 'Atru.chr7.1419' => 'acertr', 'Atru.chr7.2103' => 'acertr', 'Atru.chr7.2120' => 'acertr', 'AUR62009298' => 'cqu', 'AUR62010935' => 'cqu', 'AUR62012719' => 'cqu', 'AUR62021447' => 'cqu', 'AUR62021937' => 'cqu', 'AUR62041712' => 'cqu', 'AUR62043389' => 'cqu', 'AUR62043467' => 'cqu', 'BcaB03g13228' => 'bca', 'BcaB03g15218' => 'bca', 'BcaC05g25047' => 'bca', 'BcaC08g46155' => 'bca', 'BolC6t39139H' => 'bol', 'BraA07t31015Z' => 'bra', 'BraA08t35240Z' => 'bra', 'C06p42980' => 'bna', 'CAN.G1014.2' => 'can', 'CAN.G1774.2' => 'can', 'CAN.G335.2' => 'can', 'CANSAT25G0151' => 'cansat', 'CANSAT56G1092' => 'cansat', 'CANSAT56G3279' => 'cansat', 'CARHR012160' => 'chi', 'CARHR059760' => 'chi', 'Carub.0001s1149' => 'cru', 'Carub.0001s3381' => 'cru', 'Carub.0002s1356' => 'cru', 'Ca_00667_v3' => 'car', 'Ca_15601_v3' => 'car', 'Ca_17314_v3' => 'car', 'Ca_17347_v3' => 'car', 'Ca_21078_v3' => 'car', 'Ca_25553_v3' => 'car', 'Ca_29809_v3' => 'car', 'CBR_g48006' => 'cbr', 'Cc00_g30980' => 'ccan', 'Cc06_g10140' => 'ccan', 'Cc09_g01570' => 'ccan', 'CDE05G1502' => 'cde', 'CDE05G3153' => 'cde', 'CDE05G3288' => 'cde', 'CDE05G3525' => 'cde', 'Cfa000211' => 'cfa', 'Cfa003218' => 'cfa', 'Ciclev10003855m.g' => 'ccl', 'Ciclev10008482m.g' => 'ccl', 'Ciclev10008732m.g' => 'ccl', 'Ciclev10016134m.g' => 'ccl', 'Ciclev10016136m.g' => 'ccl', 'CiPaw.03G227600' => 'cil', 'CiPaw.08G025200' => 'cil', 'CiPaw.09G092900' => 'cil', 'CiPaw.10G071900' => 'cil', 'CiPaw.12G131200' => 'cil', 'CiPaw.12G131300' => 'cil', 'ClCG01G021910' => 'cla', 'ClCG03G004670' => 'cla', 'ClCG06G008910' => 'cla', 'ClCG10G005270' => 'cla', 'ClCG10G005290' => 'cla', 'ClCG11G002300' => 'cla', 'COL.COLO4_09678' => 'col', 'COL.COLO4_18658' => 'col', 'COL.COLO4_31789' => 'col', 'COL.COLO4_34799' => 'col', 'Cpa.g.sc3368.2' => 'cpa', 'Cpa.g.sc40.25' => 'cpa', 'Cre17.g704350' => 'cre', 'CsaV3_1G010700' => 'csa', 'CsaV3_1G019580' => 'csa', 'CsaV3_1G020720' => 'csa', 'CsaV3_2G002080' => 'csa', 'CsaV3_3G004980' => 'csa', 'CsaV3_3G005000' => 'csa', 'CsaV3_6G048970' => 'csa', 'CSS0001046' => 'camsi', 'CSS0021478' => 'camsi', 'CSS0029613' => 'camsi', 'CSS0034865' => 'camsi', 'CSS0039103' => 'camsi', 'CSS0050192' => 'camsi', 'DCAR_004477' => 'dca', 'DCAR_008161' => 'dca', 'DCAR_028678' => 'dca', 'Dinv01567' => 'din', 'Dinv13901' => 'din', 'Dinv14252' => 'din', 'Dinv20058' => 'din', 'Dinv22253' => 'din', 'Dinv31226' => 'din', 'Dinv41646' => 'din', 'Duzib150G1103' => 'dzi', 'Duzib168G0403' => 'dzi', 'Duzib187G0381' => 'dzi', 'Duzib192G0615' => 'dzi', 'Duzib235G0943' => 'dzi', 'Duzib268G1791' => 'dzi', 'ECA233G2820' => 'eca', 'ECA236G3546' => 'eca', 'ECA240G1162' => 'eca', 'EL10Ac2g04034' => 'bvu', 'EL10Ac8g18423' => 'bvu', 'EL10Ac8g20072' => 'bvu', 'Eucgr.C00588' => 'egr', 'Eucgr.C03791' => 'egr', 'Eucgr.D01335' => 'egr', 'Eucgr.D01336' => 'egr', 'Eucgr.F00747' => 'egr', 'Eucgr.F00748' => 'egr', 'Eucgr.F00749' => 'egr', 'Eucgr.L01448' => 'egr', 'Eucgr.L03428' => 'egr', 'FAN11G0165' => 'fan', 'FAN11G1161' => 'fan', 'FAN11G3560' => 'fan', 'FAN15G0197' => 'fan', 'FAN16G3016' => 'fan', 'FAN19G1252' => 'fan', 'FAN20G1448' => 'fan', 'FAN21G3772' => 'fan', 'FAN21G4024' => 'fan', 'FAN23G0317' => 'fan', 'FAN25G1199' => 'fan', 'FAN25G1493' => 'fan', 'FAN25G3690' => 'fan', 'FAN26G2053' => 'fan', 'FAN26G3039' => 'fan', 'FAN27G0559' => 'fan', 'FAN28G1806' => 'fan', 'FvH4_1g05730' => 'fve', 'FvH4_2g35710' => 'fve', 'FvH4_3g01920' => 'fve', 'FvH4_3g19740' => 'fve', 'FvH4_3g22990' => 'fve', 'Glyma.01G146300' => 'gma', 'Glyma.04G083100' => 'gma', 'Glyma.05G228500' => 'gma', 'Glyma.06G084500' => 'gma', 'Glyma.06G084550' => 'gma', 'Glyma.07G261400' => 'gma', 'Glyma.08G035400' => 'gma', 'Glyma.09G004300' => 'gma', 'Glyma.09G193800' => 'gma', 'Glyma.15G108400' => 'gma', 'Gohir.A05G025300' => 'ghi', 'Gohir.A06G065300' => 'ghi', 'Gohir.A06G094000' => 'ghi', 'Gohir.A06G148650' => 'ghi', 'Gohir.A06G207400' => 'ghi', 'Gohir.A08G242500' => 'ghi', 'Gohir.D05G026800' => 'ghi', 'Gohir.D06G063800' => 'ghi', 'Gohir.D06G093600' => 'ghi', 'Gohir.D06G154700' => 'ghi', 'Gohir.D06G213900' => 'ghi', 'Gohir.D08G263300' => 'ghi', 'Gorai.004G281400' => 'gra', 'Gorai.009G026900' => 'gra', 'Gorai.010G074500' => 'gra', 'Gorai.010G108000' => 'gra', 'Gorai.010G180800' => 'gra', 'Gorai.010G252200' => 'gra', 'GSVIVG01012714001' => 'vvi', 'GSVIVG01015339001' => 'vvi', 'GSVIVG01035641001' => 'vvi', 'GSVIVG01037671001' => 'vvi', 'GSVIVG01037672001' => 'vvi', 'HanXRQChr02g0049911' => 'han', 'HanXRQChr03g0061451' => 'han', 'HanXRQChr05g0129471' => 'han', 'HanXRQChr09g0238901' => 'han', 'HanXRQChr12g0380021' => 'han', 'Haze_06810' => 'cav', 'Haze_25800' => 'cav', 'Hma1.2p1_0019F.1_g013820' => 'hma', 'Hma1.2p1_0091F.1_g046460' => 'hma', 'Hma1.2p1_0091F.1_g046560' => 'hma', 'Hma1.2p1_0501F.1_g167505' => 'hma', 'Hma1.2p1_0590F.1_g185100' => 'hma', 'Hma1.2p1_0945F.1_g240160' => 'hma', 'HPP92_004129' => 'vpl', 'HPP92_008223' => 'vpl', 'Hund01539' => 'sun', 'Hund03848' => 'sun', 'Hund08319' => 'sun', 'Hund09231' => 'sun', 'Hund15255' => 'sun', 'Hund17870' => 'sun', 'Hund21414' => 'sun', 'Hund23461' => 'sun', 'Hund24764' => 'sun', 'Hund26243' => 'sun', 'Lalb_Chr08g0243121' => 'lal', 'Lalb_Chr09g0331361' => 'lal', 'Lalb_Chr13g0304281' => 'lal', 'Lalb_Chr20g0118731' => 'lal', 'Lalb_Chr22g0352621' => 'lal', 'Lj1C1232G4' => 'lonja', 'Lj1g0010640' => 'lja', 'Lj2g0023492' => 'lja', 'Lj4A413G12' => 'lonja', 'Lj4g0001456' => 'lja', 'Lj4g0024744' => 'lja', 'Lj6g0000498' => 'lja', 'Lj7C659G5' => 'lonja', 'Lj7C703T15' => 'lonja', 'Lsat_1_v5_gn_5_144380' => 'lsa', 'Lsat_1_v5_gn_7_16221' => 'lsa', 'Lsat_1_v5_gn_7_41340' => 'lsa', 'Manes.16G006100' => 'mes', 'Manes.16G072700' => 'mes', 'Manes.16G112000' => 'mes', 'Manes.17G026300' => 'mes', 'Mapoly0020s0109' => 'mpo', 'MBI01_g06184_MAGBIO' => 'mbi', 'MBI04_g02610_MAGBIO' => 'mbi', 'MBI09_g40167_MAGBIO' => 'mbi', 'MBI09_g46183_MAGBIO' => 'mbi', 'MBI15_g28816_MAGBIO' => 'mbi', 'MBI16_g34288_MAGBIO' => 'mbi', 'MBI19_g25025_MAGBIO' => 'mbi', 'MCO07G407' => 'mco', 'MD02G1058400' => 'mdo', 'MD03G1199000' => 'mdo', 'MD05G1348100' => 'mdo', 'MD10G1322500' => 'mdo', 'MD11G1215300' => 'mdo', 'MD15G1094500' => 'mdo', 'MD15G1192700' => 'mdo', 'Medtr0430s0010' => 'mtr', 'Medtr2g023500' => 'mtr', 'Medtr3g110185' => 'mtr', 'Medtr4g039890' => 'mtr', 'Medtr4g132260' => 'mtr', 'Medtr4g132270' => 'mtr', 'Medtr6g087120' => 'mtr', 'Medtr8g102980' => 'mtr', 'MELO3C002451.2' => 'cme', 'MELO3C004574.2' => 'cme', 'MELO3C007397.2' => 'cme', 'MELO3C008541.2' => 'cme', 'MELO3C024709.2' => 'cme', 'MELO3C025360.2' => 'cme', 'MELO3C028428.2' => 'cme', 'MELO3C028677.2' => 'cme', 'Migut.K00514' => 'egut', 'Migut.M01328' => 'egut', 'MSTRG.15993' => 'ama', 'MSTRG.6015' => 'ama', 'MSTRG.7202' => 'ama', 'Nitab4.5_0000010g0040' => 'nta', 'Nitab4.5_0000066g0120' => 'nta', 'Nitab4.5_0000151g0340' => 'nta', 'Nitab4.5_0000837g0050' => 'nta', 'Nitab4.5_0001004g0130' => 'nta', 'Nitab4.5_0002827g0100' => 'nta', 'Nitab4.5_0005564g0010' => 'nta', 'Nitab4.5_0007799g0080' => 'nta', 'Nn1g07165' => 'nnu', 'Nn2g11647' => 'nnu', 'Nn3g18150' => 'nnu', 'Oeu014929.2' => 'oeu', 'Oeu017742.1' => 'oeu', 'Oeu025272.1' => 'oeu', 'Oeu053752.2' => 'oeu', 'Oeu064904.2' => 'oeu', 'Os02g0280500' => 'osa', 'Os05g0230900' => 'osa', 'Os08g0191700' => 'osa', 'Peaxi162Scf00147g00614' => 'pax', 'Peaxi162Scf00161g00057' => 'pax', 'Peaxi162Scf00539g00613' => 'pax', 'Peaxi162Scf00665g00141' => 'pax', 'PGR004G0893' => 'pgr', 'PGR042G3664' => 'pgr', 'PGR083G1133' => 'pgr', 'PGR102G2839' => 'pgr', 'PGSC0003DMG400000302' => 'stu', 'PGSC0003DMG400009601' => 'stu', 'PGSC0003DMG400016448' => 'stu', 'Phvul.002G310700' => 'pvu', 'Phvul.003G079700' => 'pvu', 'Phvul.004G169000' => 'pvu', 'Phvul.006G149400' => 'pvu', 'Phvul.009G108700' => 'pvu', 'Potri.004G013200' => 'ptr', 'Potri.006G160600' => 'ptr', 'Potri.006G239802' => 'ptr', 'Potri.018G042100' => 'ptr', 'Potri.018G084800' => 'ptr', 'Pp3c16_11570' => 'ppa', 'Pp3c27_3630' => 'ppa', 'Pp3c4_4180' => 'ppa', 'Pp3c5_3180' => 'ppa', 'Prupe.1G449600' => 'ppe', 'Prupe.4G019400' => 'ppe', 'Prupe.4G216000' => 'ppe', 'Prupe.7G224600' => 'ppe', 'Psat1g045320' => 'psa', 'Psat1g179760' => 'psa', 'Psat1g179800' => 'psa', 'Psat1g179840' => 'psa', 'Psat4g006320' => 'psa', 'Psat5g022160' => 'psa', 'Psat7g015560' => 'psa', 'PSO210G3323' => 'pso', 'PSO210G7168' => 'pso', 'PSO541G5876' => 'pso', 'PSO675G3243' => 'pso', 'PSO700G0108' => 'pso', 'QL02p043113' => 'qlo', 'QL02p043628' => 'qlo', 'QL05p001328' => 'qlo', 'QL05p052052' => 'qlo', 'QL05p072967' => 'qlo', 'QL08p009590' => 'qlo', 'QL12p029137' => 'qlo', 'RcHm_v2.0_Chr2g0091371' => 'rch', 'RcHm_v2.0_Chr2g0110191' => 'rch', 'RcHm_v2.0_Chr4g0413001' => 'rch', 'RcHm_v2.0_Chr5g0002821' => 'rch', 'RcHm_v2.0_Chr5g0033081' => 'rch', 'RcHm_v2.0_Chr5g0040331' => 'rch', 'RcHm_v2.0_Chr5g0040381' => 'rch', 'RcHm_v2.0_Chr6g0306071' => 'rch', 'Rhsim02G0106400' => 'rsi', 'Rhsim03G0238900' => 'rsi', 'Rhsim13G0152900' => 'rsi', 'Rhsim13G0153000' => 'rsi', 'Rhsim13G0153100' => 'rsi', 'Sabra06G0187400' => 'sbr', 'Sabra11G0003800' => 'sbr', 'Sabra18G0041500' => 'sbr', 'Sabra18G0042800' => 'sbr', 'Sabra18G0073200' => 'sbr', 'SalBow6G3059' => 'sbo', 'SalBow8G5129' => 'sbo', 'Sc05g0009250' => 'sci', 'Sc06g0000760' => 'sci', 'Sc08g0007780' => 'sci', 'Sed0003250' => 'sed', 'Sed0014727' => 'sed', 'Sed0020378' => 'sed', 'Sed0023010' => 'sed', 'Sed0024006' => 'sed', 'SEGI_04121' => 'sgi', 'SGA_v2.0_scaffold7G03824' => 'sas', 'SGA_v2.0_scaffold7G03829' => 'sas', 'SMO367G0612' => 'smo', 'Solyc02g080630.4' => 'sly', 'Solyc08g066850.3' => 'sly', 'Solyc12g007310.3' => 'sly', 'Sopen02g025340' => 'spe', 'Sopen08g020830' => 'spe', 'Sopen12g003270' => 'spe', 'Sp1g10450' => 'spa', 'Sp5g22210' => 'spa', 'TAR383G0449' => 'tar', 'TAR383G0976' => 'tar', 'TAR624G0012' => 'tar', 'TAR624G0624' => 'tar', 'TAR626G0154' => 'tar', 'TAR626G1908' => 'tar', 'TAR636G3062' => 'tar', 'THA.LOC104811096' => 'tha', 'THA.LOC104818731' => 'tha', 'Thecc.06G222400' => 'tca', 'Thecc.07G033600' => 'tca', 'Thecc.09G043300' => 'tca', 'Thecc.09G104700' => 'tca', 'Thhalv10008377m.g' => 'esa', 'Thhalv10018775m.g' => 'esa', 'TPR.G13447' => 'tpr', 'TPR.G1354' => 'tpr', 'TPR.G20800' => 'tpr', 'TPR.G21457' => 'tpr', 'TPR.G23452' => 'tpr', 'TPR.G28830' => 'tpr', 'TWI32G0046' => 'twi', 'TWI34G0400' => 'twi', 'TWI34G1089' => 'twi', 'TWI38G0210' => 'twi', 'TWI38G2286' => 'twi', 'unitig_0.g2553' => 'ugi', 'unitig_748.g7966' => 'ugi', 'vmacro06239' => 'vma', 'vmacro08912' => 'vma', 'vmacro11064' => 'vma', 'vmacro15788' => 'vma', 'vmacro15791' => 'vma', 'vmacro19269' => 'vma', 'vmacro19270' => 'vma', 'vmacro22535' => 'vma', 'vmacro22905' => 'vma', 'vmacro22906' => 'vma', 'vmacro22910' => 'vma', 'vmacro23260' => 'vma', 'VMungo0251G2635' => 'vmu', 'VMungo0464G0782' => 'vmu', 'VMungo0464G1426' => 'vmu', 'VMungo0540G2290' => 'vmu', 'VMungo1215G1301' => 'vmu', 'VMungo1309G1051' => 'vmu', 'Zm00001eb109430' => 'zma', 'Zm00001eb237220' => 'zma', 'Zm00001eb237230' => 'zma', 'Zm00001eb284320' => 'zma', 'Zm00001eb413220' => 'zma', 'Zm00001eb413370' => 'zma' ) $gf_id = 'HOM05D001382' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001382' ) $data_identifier = 'HOM05D001382' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 2, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 5, 'arhy' => (int) 20, 'ath' => (int) 2, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 4, 'bol' => (int) 1, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 9, 'fan' => (int) 17, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 10, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 8, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 7, 'pso' => (int) 5, 'qlo' => (int) 7, 'rch' => (int) 8, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 12, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413370' $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